Molecular (Linkage And Association) Mapping For Abiotic Stress Tolerance In Cotton (Gossypium Hirsutum L.)

Cotton is an important crop worldwide. Global climate change is adversely affecting productivity of present day agriculture. A significant effect of global climate change is the altering of global rainfall patterns. This rainfall patterns has worsened already existing menace of drought and salt stress to agriculture. World cotton production has also affected largely by drought and salt stress. For sustained cotton production under global climate change an integrated approach, involving all available resources and techniques in a judicious manner, is needed. One potential and promising part of this integrated approach is the development of crop varieties tolerant to these abiotic stresses. Molecular (Linkage and Association) mapping techniques can be successfully used to tag the genomic regions harboring loci involved in abiotic stress tolerance in cotton to help develop cotton cultivars with promising stress tolerance. Keeping in view this objective, two projects were designed to tag genomic regions involved in drought and salinity tolerance in cotton. The summary of these two projects is given below:1-Linkage mapping for drought toleranceIncreasing scarcity of irrigational water is a major threat to sustainable production of cotton (Gossypium hirsutum L.). Identifying genomic regions contributing to abiotic stress tolerance will help develop cotton cultivars suitable for water-limited regions through molecular marker-assisted breeding.A molecular mapping F2 population was derived from an intraspecific cross of the drought sensitive G. hirsutum cv. FH-901 and drought tolerant G. hirsutum cv. RH-510. Field data were recorded on physiological traits (osmotic potential and osmotic adjustment); yield and its component traits (seedcotton yield, number of bolls/plant and boll weight); and plant architecture traits (plant height and number of nodes per plant) for F2, F2:3 and F2:4 generations under well-watered versus water-limited growth conditions. The two parents were surveyed for polymorphism using 6500 SSR primer pairs. Joinmap3.0 software was used to construct linkage map with 64 polymorphic markers. QTL analysis was performed by composite interval mapping (CIM) using QTL Cartographer2.5 software. In total,7 QTLs (osmotic potential 2, osmtic adjustment 1,seed cotton yield 1, number of bolls/plant 1, boll weight 1 and plant height 1) were identified. There were three QTLs (qtlOP-2, qtlOA-1, and qtlPH-1) detected only in water-limited conditions. Two QTLs (qtlSC-1 and qtlBW-1) were detected for relative values. Two QTLs (qtlOP-1 and qtlBN-1) were detected under well-watered conditions. Out of these 7 QTLs,3 QTLs (qtlOA-1, qtlSC-1 and qtlPH-1) can be employed successfully in MAS for molecular breeding programs aiming at developing cotton cultivars for drought tolerance.2-Association mapping for salinity toleranceSalinity is a major worldwide abiotic stress limiting agricultural production. Identification of genomic regions involved in salinity tolerance will be helpful in future molecular breeding strategies. In our present study, we design an experiment to assess the marker-trait associations under high salinity conditions. We planted 109 cotton cultivars from China and USA under the green house conditions and phenotypic data were recorded at the seedling stage (30 DAS). The cultivars were sown in polythene bags containing vermiculite. The polythene bags were arranged according to randomized complete block design with three replications with three treatments (Control, 100mM NaCl and 200mM NaCl treatments). Phenotypic data were recorded for shoot length, root length, plant length, fresh shoot weight, fresh root weight, fresh plant weight, dry shoot weight, dry root weight, dry plant weight and root-shoo ratio. The relative values of these traits were also calculated, as relative values are considered to be a good indicator of stress tolerance. Considerable variability was found among cotton cultivars under both control and salt treatments.Genotyping of 109 cotton cultivars was done by using a set of 98 SSR primer pairs with～3-5 primers/chromosome. The genotypic data obtained from SSR screening was analyzed by software STRUCTURE2.2 for estimating subgroups in population. The phenotypic data and information about the ancestry of individuals obtained from STRUCTURE2.2 software was put in the software TASSEL to determine marker-trait associations.Eight markers (NAU458, BNL3590, NAU437, NAU483, BNL3089, JESPR135, TMH05 and NAU5091) were found to be associated with all three treatments i.e., control, 100mM and 200mM NaCl. These markers were located on D1 (Chr.15), A2 (Chr.2), A2 (Chr.2), A3 (Chr.3), A4 (Chr.4), A11 (Chr.11) and D11 (Chr.21) respectively. NAU483 (A3) was associated with maximum number of traits and, especially, it was associated with more number of traits under stress conditions (both 100mM and 200mM NaCl) than under control treatment. So it is a good candidate marker for future MAS in molecular breeding programs for salinity tolerance. TMH05 (D11) was found to be associated with more number of traits under control treatment than under stress treatments. JESPR135 (All) was found to give highest phenotypic variance (R2) value of 19.1% under control treatment.41 markers were found to be associated (p≤0.05) with 200mM NaCl treatment. NAU483 (A3) was found to be associated with maximum number of traits (8) under high salinity (200mM NaCl) treatment. NAU5005 (D5) was associated with 6 traits. NAU1167 (A3) was associated with highest phenotypic variance explained (R2) value of 13.5%. Fifteen markers were found to be exclusively associated with 200mM NaCl treatment and these were not associated with either control or 100mM NaCl treatment. In this regards, markers NAU5005 (D5) and NAU980 (A11) are important as these were associated with more traits. Markers which gave relatively higher phenotypic variance explained (R2) values were NAU1042 (A5) and NAU980 (All). Fourteen markers were common in control and 200mM NaCl treatment. These markers are of special concern while considering crop improvement both under normal and high salinity stress conditions.In our association mapping study for salinity tolerance, we found two markers which were also linked to the QTLs in linkage mapping study for drought tolerance. These markers are NAU2083 and NAU3901. Association of common markers with drought and salinity tolerance throws light on the underlying common molecular mechanism for drought and salinity tolerance in cotton.